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| | ____ __ __ ___________ ______ | | |
| | / __ \/ /_ __ __/ /____ / ____/ ___// ____/ | | |
| | / /_/ / __ \/ / / / // __ \/ / \__ \/ /_ | | |
| | / ____/ / / / /_/ / // /_/ / /___ ___/ / __/ | | |
| | /_/ /_/ /_/\__, /_/ \____/\____//____/_/ | | |
| | /____/ | | |
| | | | |
| | http://compbio.mit.edu/PhyloCSF | | |
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| SOURCE DISTRIBUTION | |
| Please see our web site for more information about PhyloCSF. Compiling | |
| this software from source may be difficult for most users, because it | |
| requires an Objective Caml toolchain that's probably not already | |
| present on your system. For this reason, we provide digitally-signed | |
| 32-bit and 64-bit Linux executables on our web site. | |
| The source distribution is divided into a library, CamlPaml, containing | |
| generic infrastructure for phylogenetic rate models, and a program | |
| implementing the PhyloCSF-specific models and driver program. With | |
| additional development, the CamlPaml library will eventually be | |
| released as a separate entity, but for now it is just part of this | |
| distribution. | |
| Here are the steps to build the source: | |
| [1A] Install various dependencies (Ubuntu 11.10+) | |
| Install these packages using apt-get: | |
| ocaml-findlib libocamlgsl-ocaml-dev libbatteries-ocaml-dev make | |
| [1B] Install various dependencies (other Linux, Mac OS X) | |
| * Objective Caml 3.11+, with native code compiler | |
| * OCaml findlib | |
| * OCaml Batteries Included 1.20+ | |
| - GNU Scientific Library | |
| - ocamlgsl 0.60 http://oandrieu.nerim.net/ocaml/gsl/ocamlgsl-0.6.0.tar.gz | |
| * These can be set up using GODI: http://godi.camlcity.org/ | |
| [2] Configure OCaml findlib | |
| If you installed findlib (OCaml's package manager) using the Ubuntu | |
| packages, or another method that led to system-wide installation, you | |
| must set some environment variables to make it use a directory to which | |
| you have write access. (Alternatively, you can complete the subsequent | |
| steps as root, e.g. using sudo) | |
| export OCAMLPATH=$HOME/opt/lib/ocaml # or whatever | |
| mkdir -p $OCAMLPATH | |
| export OCAMLFIND_DESTDIR=$OCAMLPATH | |
| To verify your configuration, run | |
| ocamlfind printconf | |
| "Packages will be installed in" should be a directory you can write to, | |
| and that same directory should appear in "Search path". | |
| [3] Compile PhyloCSF | |
| Now just run 'make' in this directory. This will build and install the | |
| CamlPaml library, then compile the PhyloCSF executable and copy it to | |
| PhyloCSF.ARCH in this directory, where e.g. ARCH = Linux.x86_64. |